CMA Ordering

Ordering CMA testing is similar to ordering other types of genetic tests. As with other genetic tests, you need to consider which labs offer the test that will be most useful for your patient, whether your patient’s insurance requires preauthorization for testing, and what information the lab requires. Here we address the different testing options available and provide information to help you get the most out of the testing.

What types of CMA testing are available?

There are three types of CMA testing, which are summarized below. We include BAC array for historical perspective, but current standard of practice involves oligo, SNP, or a combination of the two platforms. Lab specialists can often recommend a specific CMA type for your clinical purpose.

(bacterial artificial chromosome)

  • No longer standard of practice
  • Limited detection of very small variants
  • Poor ability to estimate boundaries of variants
  • Patients with a negative BAC array may benefit from Oligo and/or SNP testing

Oligo (oligonucleotide)

  • Detects smaller variants than BAC
  • Provides highly accurate estimate of boundaries of a copy number variant (CNV)

(single nucleotide polymorphism)

  • Detects smaller variants than BAC, similar to Oligo
  • Provides highly accurate estimate of boundaries of a copy number variant (CNV)
  • Detects triploidy
  • Detects regions of excessive homozygosity*, suggestive of risk of recessive disease and imprinting disorders
  • SNP CMA is NOT the same as SNP testing for common disease susceptibility variants

What other parameters are important?


CMA tests vary in terms of the number of probes used for a given genomic region, and the amount of overlap between those probes. On lab materials, look for references to probe “density” or “spacing”. All CMA testing involves some gaps in the genome.


  • Some array designs have a genome-wide backbone enriched with more probes in areas of clinical significance. 
  • Genome-wide array: Analysis includes regions across the entire genome without specific known association to clinical features. This approach increases the likelihood of finding a pathogenic variant, but also increases the chance of a variant of uncertain significance.
  • Targeted array: Analysis is limited to regions that are most likely to be associated with a particular clinical presentation. This approach is less likely to identify variants of unknown significance, but may miss causative variants outside the targeted region.

What do I need to know about labs?

Where should I look for labs?

Many laboratories that offer CMA testing have comprehensive websites that provide educational and practical information about their testing options. Some will offer CMA as part of a much larger genetic testing menu, while others specialize in various types of chromosome analysis or genome-wide testing. Consider the following directories and resources:

  • GeneTests Laboratory Directory. This resource, along with GeneReviews disease summaries, is provided by the National Center for Biotechnology Information (NCBI). 
  • Genetic Testing Registry. Another resource of the NCBI, this registry provides information about genetic tests available for specific conditions. 
  • Labs already familiar to you. Your institution’s cytogenetics lab may offer its own CMA testing panel, or they may have an established relationship with a CMA lab. Large laboratory referral services offer CMA testing. Check with other labs you use for specialty testing to see if they offer CMA as well.
  • The patient’s health insurance. Some insurance companies have preferred labs for specialty testing. See the section on working with insurance companies below.

What criteria should I use when selecting a CMA lab?

Select a reputable, CLIA certified lab that can work with your institution and the patient’s insurance company. In addition, consider how much support you and your patient will need through different stages of the testing process.
Criteria in selecting a lab to consider are

  • How comprehensive is the testing?
  • Availability of guidance and support
  • Insurance and billing protocols (see also section below on insurance)
  • Reporting practices
  • Protocols for parental testing

Provide appropriate and sufficient clinical information to the lab

Because our understanding of copy number variants is still evolving, interpretation of CMA findings relies heavily on the clinical context. CMA labs may ask for more detailed information than typical for other tests. The more information you can provide the lab, the more likely it is that their report will be clear and useful. A few extra minutes providing information up front can speed turn-around time and improve interpretation.

What to expect

  • Turn around time range from 2-6 weeks; samples can sometimes be prioritized.
  • Reports may be issued directly to you or to the referral lab – check to be sure you received the full interpretation; results are typically more than one page.
  • The lab may call to  clarify clinical information for interpretation purposes.

What do I need to know about insurance requirements

Because it is now recommended as a first tier test for certain indications, insurance companies are becoming more familiar with CMA, and most will cover the test. However, an insurance provider may not have a clear policy for the use of CMA for atypical clinical indications. Resources (such as templates for letters of medical necessity) are available to help you make a case for coverage of testing when necessary. Some labs provide assistance with insurance filing and prior authorization. The cost of CMA will likely decrease as technology improves. However, most genetic testing is still relatively expensive compared to more routine lab tests. Families should be informed of the cost of the test so they can determine the proportion that will be their responsibility.